› 6s53

X-ray diffraction
2.8Å resolution

Crystal structure of TRIM21 RING domain in complex with an isopeptide-linked Ube2N~ubiquitin conjugate

Released:
DOI: 10.2210/pdb6s53/pdb
PDB entry 6s53 coloured by chain, front view.
PDB entry 6s53 coloured by chain, side view.
PDB entry 6s53 coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
A tri-ionic anchor mechanism drives Ube2N-specific recruitment and K63-chain ubiquitination in TRIM ligases.
Kiss L, Zeng J, Dickson CF, Mallery DL, Yang JC, McLaughlin SH, Boland A, Neuhaus D, James LC
Nat Commun 10 4502 (2019)
PMID: 31582740

Function and Biology Details

Reactions catalysed: 
S-ubiquitinyl-[E1 ubiquitin-activating enzyme]-L-cysteine + [E2 ubiquitin-conjugating enzyme]-L-cysteine = [E1 ubiquitin-activating enzyme]-L-cysteine + S-ubiquitinyl-[E2 ubiquitin-conjugating enzyme]-L-cysteine
S-ubiquitinyl-[E2 ubiquitin-conjugating enzyme]-L-cysteine + [acceptor protein]-L-lysine = [E2 ubiquitin-conjugating enzyme]-L-cysteine + N(6)-ubiquitinyl-[acceptor protein]-L-lysine
Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
hetero hexamer (preferred)
PDBe Complex ID:
PDB-CPX-143419 (preferred)
Entry contents:
3 distinct polypeptide molecules
Macromolecules (3 distinct):
Ubiquitin-conjugating enzyme E2 N Chains: C, E, I, K
Molecule details ›
Chains: C, E, I, K
Length: 152 amino acids
Theoretical weight: 17.13 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli BL21
UniProt:
  • Canonical: P61088 (Residues: 1-152; Coverage: 100%)
Gene names: BLU, UBE2N
Sequence domains: Ubiquitin-conjugating enzyme
Ubiquitin Chains: D, F, J, L
Molecule details ›
Chains: D, F, J, L
Length: 76 amino acids
Theoretical weight: 8.58 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: P0CG48 (Residues: 609-684; Coverage: 11%)
Gene name: UBC
Sequence domains: Ubiquitin family
E3 ubiquitin-protein ligase TRIM21 Chains: A, B, G, H
Molecule details ›
Chains: A, B, G, H
Length: 85 amino acids
Theoretical weight: 9.51 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli BL21
UniProt:
  • Canonical: P19474 (Residues: 1-85; Coverage: 18%)
Gene names: RNF81, RO52, SSA1, TRIM21
Sequence domains: Zinc finger, C3HC4 type (RING finger)

Ligands and Environments

2 bound ligands:
Ligand ZN 8 x ZN
Ligand MPD 1 x MPD
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: DIAMOND BEAMLINE I04
Spacegroup: P1
Unit cell:
a: 49.75Å b: 83.31Å c: 86.75Å
α: 89.9° β: 89.05° γ: 88.7°
R-values:
R R work R free
0.209 0.209 0.25
Expression systems:
  • Escherichia coli BL21
  • Escherichia coli

Quick links

Citations

1 review citation

TRIMs: selective recruitment at different steps of the NF-κB pathway-determinant of activation or resolution of inflammation.
Roy et al. (2021)
13 other articles

5 mentions without citation

PROTAC targeted protein degraders: the past is prologue.
Békés et al. (2022)
4 more